avoid confusing git with a modified ctime in clean filter

Linking the file to the tmp dir was not necessary in the clean
filter, and it caused the ctime to change, which caused git to think
the file was changed. This caused git status to get slow as it kept
re-cleaning unchanged files.

Assistant/Threads/Committer.hs

@@ -268,11 +268,15 @@ handleAdds havelsof delayadd cs = returnWhen (null incomplete) $ do
 	direct <- liftAnnex isDirect
 	unlocked <- liftAnnex versionSupportsUnlockedPointers
 	let lockingfiles = not (unlocked || direct)
+	let lockdownconfig = LockDownConfig
+		{ lockingFile = lockingfiles
+		, hardlinkFileTmp = True
+		}
 	(pending', cleanup) <- if unlocked || direct
 		then return (pending, noop)
 		else findnew pending
 	(postponed, toadd) <- partitionEithers
-		<$> safeToAdd lockingfiles havelsof delayadd pending' inprocess
+		<$> safeToAdd lockdownconfig havelsof delayadd pending' inprocess
 	cleanup
 
 	unless (null postponed) $
@@ -283,7 +287,7 @@ handleAdds havelsof delayadd cs = returnWhen (null incomplete) $ do
 			catMaybes <$>
 				if not lockingfiles
 					then addunlocked direct toadd
-					else forM toadd (add lockingfiles)
+					else forM toadd (add lockdownconfig)
 		if DirWatcher.eventsCoalesce || null added || unlocked || direct
 			then return $ added ++ otherchanges
 			else do
@@ -310,15 +314,15 @@ handleAdds havelsof delayadd cs = returnWhen (null incomplete) $ do
 		| c = return otherchanges
 		| otherwise = a
 
-	add :: Bool -> Change -> Assistant (Maybe Change)
-	add lockingfile change@(InProcessAddChange { lockedDown = ld }) = 
+	add :: LockDownConfig -> Change -> Assistant (Maybe Change)
+	add lockdownconfig change@(InProcessAddChange { lockedDown = ld }) = 
 		catchDefaultIO Nothing <~> doadd
 	  where
 	  	ks = keySource ld
 		doadd = sanitycheck ks $ do
 			(mkey, mcache) <- liftAnnex $ do
 				showStart "add" $ keyFilename ks
-				ingest $ Just $ LockedDown lockingfile ks
+				ingest $ Just $ LockedDown lockdownconfig ks
 			maybe (failedingest change) (done change mcache $ keyFilename ks) mkey
 	add _ _ = return Nothing
 
@@ -332,15 +336,19 @@ handleAdds havelsof delayadd cs = returnWhen (null incomplete) $ do
 		ct <- liftAnnex compareInodeCachesWith
 		m <- liftAnnex $ removedKeysMap isdirect ct cs
 		delta <- liftAnnex getTSDelta
+		let cfg = LockDownConfig
+			{ lockingFile = False
+			, hardlinkFileTmp = True
+			}
 		if M.null m
-			then forM toadd (add False)
+			then forM toadd (add cfg)
 			else forM toadd $ \c -> do
 				mcache <- liftIO $ genInodeCache (changeFile c) delta
 				case mcache of
-					Nothing -> add False c
+					Nothing -> add cfg c
 					Just cache ->
 						case M.lookup (inodeCacheToKey ct cache) m of
-							Nothing -> add False c
+							Nothing -> add cfg c
 							Just k -> fastadd isdirect c k
 
 	fastadd :: Bool -> Change -> Key -> Assistant (Maybe Change)
@@ -416,12 +424,12 @@ handleAdds havelsof delayadd cs = returnWhen (null incomplete) $ do
  -
  - Check by running lsof on the repository.
  -}
-safeToAdd :: Bool -> Bool -> Maybe Seconds -> [Change] -> [Change] -> Assistant [Either Change Change]
+safeToAdd :: LockDownConfig -> Bool -> Maybe Seconds -> [Change] -> [Change] -> Assistant [Either Change Change]
 safeToAdd _ _ _ [] [] = return []
-safeToAdd lockingfiles havelsof delayadd pending inprocess = do
+safeToAdd lockdownconfig havelsof delayadd pending inprocess = do
 	maybe noop (liftIO . threadDelaySeconds) delayadd
 	liftAnnex $ do
-		lockeddown <- forM pending $ lockDown lockingfiles . changeFile
+		lockeddown <- forM pending $ lockDown lockdownconfig . changeFile
 		let inprocess' = inprocess ++ mapMaybe mkinprocess (zip pending lockeddown)
 		openfiles <- if havelsof
 			then S.fromList . map fst3 . filter openwrite <$>